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CCRGeneticsBranch / Oncogenomics_NF_WF

https://ccrgeneticsbranch.github.io/Oncogenomics_NF_WF/
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STAR fusion #3

Closed kopardev closed 1 year ago

kopardev commented 1 year ago

Add star fusion to the pipeline.

kopardev commented 1 year ago

STAR fusion required a Trinity database to be downloaded from [here] (https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/) Downloaded on biowulf for local access and pushed to s3 bucket for AGC access. Used this version "GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz"

kopardev commented 1 year ago

What is the purpose of STARens rule ... we don't need to re-align with STAR ... Chimeric junctions output is already created by STAR rule. Can you explain this to me, @vinegang ??

kopardev commented 1 year ago

Ran into this issue..now increasing RAM to 120GB

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kopardev commented 1 year ago

Docker was missing JSON::XS perl module .. added in v1.3

vinegang commented 1 year ago

This Issue is fixed several months ago. Entire fusion module is working without any errors.